089c09e98db52e92da694ab1a0c8891c1a7fd3e8 gperez2 Thu Apr 2 15:50:07 2026 -0700 Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM. diff --git src/hg/makeDb/trackDb/human/affy120K.html src/hg/makeDb/trackDb/human/affy120K.html index 9a2043f72ac..e6b73e4dfc3 100644 --- src/hg/makeDb/trackDb/human/affy120K.html +++ src/hg/makeDb/trackDb/human/affy120K.html @@ -1,63 +1,63 @@ <H2>Description</H2> <P>This track shows locations of the Single Nucleotide Polymorphisms on the Affymetrix 120K SNP Genotyping Array. The SNPs in this track include all of the markers from the array that have been successfully mapped against the current assembly.</P> <P>The SNPs were selected from public domain databases or the Perlegen SNP database. Genotypes for these markers were generated at Affymetrix using GeneChip(r) DNA analysis technology.</P> <P>During sample preparation, an <B>enzyme</B> is used to fragment the genomic DNA into smaller pieces. The restriction endonucleases <I><B>HindIII</B></I> and <I><B>XbaI</B></I> have been used to generate this data.</P> <P>Genotypes are reported as pairs of basecalls representing the two observed alleles. Individual genotypes for which no call was made are labeled 'NC'. A minimum of 46 genotype calls in the set of 54 individuals are included for each SNP.</P> <P><B>Allele Frequency</B> for the 'A' allele is two times the number of 'AA' calls plus the number of 'AB' calls, divided by two times the total number of calls. Allele Frequency for the 'B' allele is two times the number of 'BB' calls plus the number of 'AB' calls, divided by two times the total number of calls. The <B>Minimum Allele Frequency</B> is the lesser of these two values. <B>Heterozygosity</B> is two times the product of the two allele frequencies.</P> <H2>Credits</H2> <P>Thanks to <A HREF="https://www.ncbi.nlm.nih.gov/SNP">dbSnp</A> at the NCBI for providing the public SNPs, and thanks to <A HREF="http://www.perlegen.com">Perlegen Sciences, Inc.</A> for providing additional SNPs from their database. Additional information about the Perlegen SNP discovery process can be found in <a href="http://www.sciencemag.org/cgi/content/abstract/294/5547/1719"> <i>Science</i> <b>294</b>: 1719-1723 (2001)</a>: <p> <b>Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21</b> <br> N. Patil, A. J. Berno, D. A. Hinds, W. A. Barrett, J. M. Doshi, C. R. Hacker, C. R. Kautzer, D. H. Lee, C. Marjoribanks, D. P. McDonough, B. T. N. Nguyen, M. C. Norris, J. B. Sheehan, N. Shen, D. Stern, R. P. Stokowski, D. J. Thomas, M. O. Trulson, K. R. Vyas, K. A. Frazer, S. P. A. Fodor, and D. R. Cox. -<P>Thanks to <A HREF="http://www.affymetrix.com">Affymetrix, Inc.</A> +<P>Thanks to <A HREF="https://www.affymetrix.com">Affymetrix, Inc.</A> for developing the genotyping array and providing the genotype data for 54 individuals. For more details on this genotyping assay, please see the supplemental information on the <A -HREF="http://www.affymetrix.com/support/technical/sample_data/genotyping_data.affx">Affymetrix +HREF="https://www.affymetrix.com/support/technical/sample_data/genotyping_data.affx">Affymetrix 120K SNP</A> product.</P> <H2>Terms of Use</H2> <P>Please see the <A HREF="https://www.affymetrix.com:443/site/terms.affx">Terms and Conditions</A> for the use of this data at the <A -HREF="http://www.affymetrix.com">Affymetrix, Inc.</A> site.</P> +HREF="https://www.affymetrix.com">Affymetrix, Inc.</A> site.</P>